Though I have not tried Win32::Process as I have some limitation to add new module in my application. But as you suspected the application is not creating the window as I am able to see the command that I gave in system in perl getting executed in command prompt window. I am able to rectify this in Linux by adding a extra argument $args
= " 2>&1 >/dev/null"; which is passing the output to /dev/null and do not show on prompt. Similar way I want it in Windows so that it do not show command prompt and complete the command execution in background.